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    LOC130007253 ATAC-STARR-seq lymphoblastoid silent region 4170 [ Homo sapiens (human) ]

    Gene ID: 130007253, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130007253
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 4170
    Gene type
    biological region
    Feature type(s)
    regulatory: silencer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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    Genomic context

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    See LOC130007253 in Genome Data Viewer
    Location:
    chromosome: 12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6555770..6556009)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6566129..6566368)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6664936..6665175)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene non-SMC condensin I complex subunit D2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6641915-6642688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6642689-6643462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6643463-6644236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6645785-6646558 Neighboring gene GAPDH divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5866 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6658582-6659082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6659083-6659583 Neighboring gene intermediate filament family orphan 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6660263-6660762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6661035-6661552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663184-6663684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663685-6664185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4171 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6677307-6677928 Neighboring gene NOP2 nucleolar protein Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene chromodomain helicase DNA binding protein 4 Neighboring gene small Cajal body-specific RNA 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_186588.1 

      Range
      101..340
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      6555770..6556009
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      6566129..6566368
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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